Date	Version	Changes
02-21-2018	4.0	- read.pcadapt generates bed files instead of pcadapt files.
		- Computation of PCA is based on the package RSpectra.
		- Missing values are handled by specifying vector-matrix operation in RSpectra that accounts for missing values.
		- Includes LD thinning to compute PCs.
		- No more dependency to RcppArmadillo
		- For Pooled-seq data, use Mahalanobis distances based on PCA loadings, no more simulations of individuals genotypes
01-15-2017	3.1.0	- Switch from C/Lapack to Rcpp/RcppArmadillo.
		- pcadapt can take genotype matrices as input.
		- Modified code for binomial sampling.
		- pcadapt argument clean.files is now deprecated.
		- pcadapt argument output.filename is now deprecated.
		- read.pcadapt argument local.env is now deprecated.
		- Latest update of vcfR taken into account.
12-20-2016	3.0.4	- Method based on sampling genotypes added to handle pooled-sequencing.
10-06-2016	3.0.3	- Option type="vcfR" has been added to read.pcadapt to overcome some conversion issues occurring with VCF files.
		- Argument transpose is now deprecated. Read section A for more details.
06-13-2016	3.0.2	- The function get.pc has been added. For each SNP, it returns the most correlated principal component.
06-01-2016	3.0.1	- The read4pcadapt is now deprecated, it is now called read.pcadapt.
		- Using the pop option when plotting scores now provides the color legend.
04-04-2016	3.0	- All analyses are now included in the R package. Users should not use the C software PCAdapt fast anymore.
		- Big datasets can be handled directly within the R session.
		- read4pcadapt now converts files to the pcadapt format.
		- The first argument of pcadapt can be either a small genotype matrix or the output of read4pcadapt.
02-12-2016	2.2	- The Mahalanobis distance is now estimated from the z-scores rather than the loadings.
		- Make sure you have downloaded the latest version of the C software PCAdapt (last updated on February 11, 2016).
01-05-2016	2.1.1	- Bug fix: vignette header added.
12-18-2015	2.1	- The scaling of the SNP before computing PCA has been changed. Instead of using standard deviation, we now use the square root of \(p(1-p)\) (haploid data) or of \(2p(1-p)\) (diploid data) where \(p\) is the minimum allele frequency.
		- Bug fix: the genomic inflation factor has been corrected when K=1.
		- Bug fix: a problem due to high proportion of missing data slowing the program has been fixed.
		- Argument "minmaf" has been replaced with "min.maf".
	2.0.1	- Vignette corrected: when reading output from the software PCAdapt, we do not mention the deprecated argument PCAdapt in the function pcadapt.
		- Bug fix: an issue occurring when reading outputs from PCAdapt has been fixed.
		- We mention in the vignette how to use Pool-seq data with the C software PCAdapt fast.
	2.0	- The default test statistic is not the communality statistic anymore but the Mahalanobis distance.
		- Test statistic for Pool-seq data.